It's by design. Sorting categories turned out to be tricky, so we decided to hide the categories when sorting - i.e. only sorting entries is possible.
(Think I should expand the answer a bit more: There are two types of relations between nodes. The "primary" ones, which can't be sorted, and the "linked" ones, which can be sorted now. I was talking about the primary ones (which should be the ones in the questions) - and they should be the most common ones as well)
However I agree that sorting categories makes senses in cases like yours. We might try to improve the UX by allowing sorting categories in some way, but that's not a promise :)
Why can't you just display the SortOrder field in the Commerce UI part for a node? You can access the SortOrder via Commerce Manager and setting that value changes the sort order.
/Kristoffer
"just display" can be more complicated than it sounds.
And keep in mind we (have to) work on a framework level. Some changes can be done at implementation level as long as it gets a job done, but we are not allowed to release an incomplete, half baked solution. Such changes would never get through UX reviews.
Of course, and I guess you had some good reason not to move SortOrder to the new UI when it was created. Let just hope that it will be there in some shape in the future.
I just updated my Commerce project to version 11 and wanted to sort categories by my custom order through UI, but once I switch new "Sort mode," all categories disappear. It works for products, but not for categories.
Is it a bug?
P.S. One of the reasons for upgrading was category sorting as the customer wants to order sub-categories displayed in the navigation in a custom order. Product ordering seems useless as no one will go to sort those manually unless there are only a few products.